Novel nucleic acid-guided nucleases

Abstract

The present disclosure provides novel nucleic acid-guided nucleases and methods of using the nucleases for genome editing. The present disclosure further provides a system for editing a target region in a genome comprising a nucleic acid-guided nuclease, a heterologous guide nucleic acid for complexing with the nucleic acid-guided nuclease, and an editing polynucleotide configured to bind to the target region.

What is claimed is: 
     
         1 . An engineered, non-naturally occurring targetable nuclease system comprising: (a) a nucleic acid-guided nuclease, comprising a nuclease polypeptide having at least 95% sequence identity to a sequence selected from SEQ ID NO: 2-273, and (b) at least one engineered guide polynucleotide designed to form a complex with the nuclease and comprising a guide sequence, wherein the guide sequence is designed to hybridize with a target sequence in a eukaryotic cell, and (c) the complex of the nuclease and the guide polynucleotide do not naturally occur. 
     
     
         2 . The targetable nuclease system of  claim 1 , wherein the nuclease polypeptide has at least 97% sequence identity to a sequence selected from SEQ ID NO: 2-273. 
     
     
         3 . The targetable nuclease system of  claim 2 , wherein the nuclease polypeptide has less than 100% sequence identity to SEQ ID NO: 2-273. 
     
     
         4 . The targetable nuclease system of  claim 1 , wherein the nuclease polypeptide has at least 95% sequence identity to a sequence selected from SEQ ID NO: 123, 116, 146, 43, 254, and 175. 
     
     
         5 . The targetable nuclease system of  claim 1 , wherein the nuclease polypeptide has at least 95% sequence identity to a sequence selected from SEQ ID NO: 123, 146, 254, and 175. 
     
     
         6 . The targetable nuclease system of  claim 5 , wherein the nuclease polypeptide comprises a sequence selected from SEQ ID NO: 815-822 
     
     
         7 . The targetable nuclease system of  claim 6 , wherein the nuclease polypeptide comprises sequences of SEQ ID NO: 815-822 
     
     
         8 . The targetable nuclease system of  claim 1 , wherein the nuclease polypeptide has at least 95% sequence identity to a sequence selected from SEQ ID NO: 116 and 43. 
     
     
         9 . The targetable nuclease system of  claim 1 , wherein the nuclease polypeptide comprises a sequence of SEQ ID NO: 123. 
     
     
         10 . The targetable nuclease system of  claim 1 , wherein the nuclease polypeptide comprises a sequence of SEQ ID NO: 116. 
     
     
         11 . The targetable nuclease system of  claim 1 , wherein the nuclease polypeptide comprises a sequence of SEQ ID NO: 146. 
     
     
         12 . The targetable nuclease system of  claim 1 , wherein the nuclease polypeptide comprises a sequence of SEQ ID NO: 32. 
     
     
         13 . The targetable nuclease system of  claim 1 , wherein the nuclease polypeptide comprises a sequence of SEQ ID NO: 254. 
     
     
         14 . The targetable nuclease system of  claim 1 , wherein the nuclease polypeptide comprises a sequence of SEQ ID NO: 175. 
     
     
         15 . The targetable nuclease system of  claim 1 , wherein the nuclease polypeptide is fused to a fusion peptide. 
     
     
         16 . The targetable nuclease system of  claim 15 , wherein the fusion peptide is a signal peptide fused in-frame to the nuclease polypeptide. 
     
     
         17 . The targetable nuclease system of  claim 15 , wherein the fusion peptide is a nuclear localization sequence fused to the nuclease polypeptide. 
     
     
         18 . The targetable nuclease system of  claim 17 , wherein the nuclear localization sequence has a sequence selected from SEQ ID NO: 628-631. 
     
     
         19 . The targetable nuclease system of  claim 1 , wherein the nuclease polypeptide is originated from  Acidaminococcus massiliensis, Acidaminococcus  sp.,  Acinetobacter indicus, Agathobacter rectalis, Anaerovibrio lipolyticus, Bacteroidales bacterium, Bacteroides galacturonicus, Bacteroides plebeius, Bacteroidetes bacterium, Butyrivibrio fibrisolvens, Butyrivibrio hungatei, Butyrivibrio  sp.,  Candidatus Falkowbacteria bacterium, Candidatus Falkowbacteria bacterium, Candidatus Gottesmanbacteria bacterium, Candidatus Jacksonbacteria bacterium, Candidatus Magasanikbacteria bacterium, Candidatus Moranbacteria bacterium, Candidatus Pacebacteria bacterium, Candidatus Roizmanbacteria bacterium, Candidatus Ryanbacteria bacterium, Candidatus Saccharibacteria bacterium, Candidatus Sungbacteria bacterium, Candidatus Uhrbacteria bacterium, Candidatus Wildermuthbacteria bacterium, Candidatus Yonathbacteria bacterium, Catenovulum  sp.,  Clostridiales bacterium, Clostridium  sp.,  Coprococcus eutactus, Coprococcus  sp.,  Deltaproteobacteria bacterium, Elizabethkingia  sp.,  Eubacteriaceae bacterium, Eubacterium eligens, Eubacterium rectale, Eubacterium  sp.,  Eubacterium ventriosum, Fibrobacter  sp.,  Fibrobacter succinogenes, Firmicutes bacterium, Flavobacterium branchiophilum, Francisella hispaniensis, Francisella novicida, Francisella philomiragia, Francisella tularensis, Lachnospiraceae bacterium, Lachnospira pectinoschiza, Lentisphaeria bacterium, Leptospiraceae bacterium, Leptospira  sp.,  Moraxella bovis, Moraxella bovoculi, Moraxella lacunata, Moraxella ovis, Moraxella  sp.,  Muribaculaceae bacterium, Patescibacteria group bacterium, Phycisphaerae bacterium, Phycisphaerales bacterium, Porphyromonadaceae bacterium, Porphyromonas crevioricanis, Prevotella brevis, Prevotellaceae bacterium, Prevotella copri, Prevotellamassilia  sp.,  Prevotella ruminicola, Prevotella  sp.,  Prolixibacteraceae bacterium, Pseudobutyrivibrio  sp.,  Pseudobutyrivibrio xylanivorans, Psychrobacter  sp.,  Ruminococcaceae bacterium, Ruminococcus  sp.,  Sedimentisphaera cyanobacteriorum, Sneathia amnii, Spirochaetia bacterium, Succinivibrionaceae bacterium , or  Treponema  sp. 
     
     
         20 . A polynucleotide comprising a first polynucleotide segment encoding the nucleic acid-guided nuclease having at least 95% sequence identity to a sequence selected from SEQ ID NO: 2-273. 
     
     
         21 . The polynucleotide of  claim 20 , further comprising a second polynucleotide segment encoding a fusion peptide. 
     
     
         22 . A vector encoding the nucleic acid-guided nuclease, comprising the polynucleotide of  claim 20 . 
     
     
         23 . A host cell comprising the polynucleotide of  claim 20 . 
     
     
         24 . A method of generating a nucleic acid-guided nuclease comprising the steps of:
 culturing the host cell of  claim 23 , and   isolating the nucleic acid-guided nuclease from the host cell culture.   
     
     
         25 . A method of modifying a target region of a eukaryotic or prokaryotic genome, comprising the steps of:
 a. contacting a sample comprising the target region with
 i. a nucleic acid-guided nuclease having at least 90% sequence identity to a sequence selected from the group consisting of SEQ ID NO: 2-273, and 
 ii. a guide nucleic acid complexed with the nucleic acid-guided nuclease, and 
   b. allowing the nucleic acid-guided nuclease to modify the target region.